Waking Dreams
by Hah and Mer
Summary: The Genii return to Atlantis in force, and Elizabeth must deal with a tragic loss. John and Liz friendship, angst, and plenty of Shep whumping! Character death warning. COMPLETE.
1. Chapter 1

**Title:** Waking Dreams  
**Author:** Mer  
**Genre:** General  
**Warnings:** Character death, non-graphic violence  
**Season/Spoilers:** season 1, vaguely season 2, but no spoilers, really  
**Summary:** Elizabeth Weir's reflections on the fall of Atlantis (character death, angst, friendshippy)  
**Disclaimer:** I don't own any of the characters. I'm just borrowing them for a bit.

**AN:** This one's a solo effort by Mer, who is now addicted to fic'ing thanks to Firegate :P Thanks a ton to Hah who beta'd and came up with the title :D And Em for her ideas too ;)

- - - - -

**Waking Dreams**

By Mer

In her darkest hours, when Elizabeth had imagined the city of Atlantis falling, it had always been to the Wraith - not to other humans who should have been allies against a common enemy. She had seen enough of humans killing each other back on Earth; was this destined to be their fate on every planet, in every galaxy?

They had come one quiet night; one hundred and twenty Genii soldiers stormed the gate, killing everyone in their path. We never did find out how they'd acquired the IDC code; it didn't matter now. "Bring me Major Sheppard" were the first words Kolya had spoken.

They'd brought him into the control room with his hands cuffed behind his back, lip bloodied and swollen. No chance for heroics this time. He grinned at Kolya and reminded him of the score last time they'd gone up against each other. Kolya gave him the score _this_ time and John spat in his face. That was the John Sheppard she wanted to remember, defiant to the end.

She and a handful of survivors managed to set the self-destruct before making their escape; the Genii had no interest in Earth, but in their unskilled hands Atlantis would surely fall to the Wraith soon. They took a Jumper to the closest inhabitable planet where they'd survived for nine days until the Daedalus picked up their signal and brought them home.

Home. Was this home? Or was Atlantis? It didn't matter. Home was her team; Rodney, Carson, Teyla, Aiden, even Ronon had become like part of their family. John. She tried to avoid his name because the images it brought back were too painful. Instead, she tried to remember his infectious smile, the way his eyes lit up when they discovered a shiny new gadget, or the way one little smirk could convince her of practically anything.

Sometimes it all felt like a dream; being whisked away to another galaxy, doing and seeing things she could never have imagined, then being unceremoniously deposited back here on Earth, still forbidden to talk about their highly classified mission. It was almost as if the last two years had never happened. But the images, they were too real. Bodies of dozens of soldiers who had fallen defending that place they'd grown to call home. John Sheppard, chest bloodied and full of Genii bullets, executed right before her eyes for Kolya's petty revenge.

So many had given their lives for the science, the technology, the medicinal knowledge they'd brought back that was already saving countless lives. Maybe one day it would help save the planet from the new enemies Earth had gained in the expedition's absence. She flipped on the news and wondered if this world was even worth saving. Had she always been this cynical?

Maybe Atlantis had been real and this place was just a dream. Elizabeth turned off the tv, closed her eyes, and hoped to wake up.

- - - - -


	2. Chapter 2

**Title:** Waking Dreams  
**Author:** Mer  
**Genre:** General  
**Warnings:** Character death, some violence, and a bit of coarse language  
**Season/Spoilers:** season 1, vaguely season 2, but no spoilers, really  
**Summary:** Elizabeth Weir relives a Genii invasion of Atlantis that resulted in tragedy. Plenty of Shep whumping. (character death, angst, John/Liz friendship)  
**Disclaimer:** I don't own any of the characters. I'm just borrowing them for a bit.

**AN:** Thanks a TON for all the wonderful feedback I received here and other places for this fic! It inspired me to delve a bit deeper, in the form of a flashback. Oh, and there's WAY more whump ;) This is the first of three additional chapters I've planned.

Thanks again to Hah and Em for putting up with my constant pestering, for beta'ing, and for being Shep whump addicts ;)

- - - - -

**Waking Dreams**

By Mer

- Chapter 2 -

(_flashback_)

Dr. Elizabeth Weir rubbed her eyes. She was up late again, working on some reports to send back to the SGC. She didn't need to stay up this late to work on them, but she couldn't sleep anyways when one of her teams was overdue. She considered seeing what John was up to. He could be a night owl himself, and he, too, worried about their teams. Her thoughts were interrupted by a call over her radio.

"Dr. Weir? We've got an offworld activation."

"Is it Sgt. Stackhouse's team?"

"Yes, Ma'am. Just receiving his IDC now. He says they're doing fine."

Elizabeth sighed with relief. "Lower the shield."

- - - - -

In the control room, the two officers manning the gate received Dr. Weir's go-ahead and lowered the shield. They watched as Sgt. Stackhouse stepped through the gate, followed by three men in the grey uniforms of Atlantis. A moment after stepping through the gate, Stackhouse yelled up to the control room.

"Raise the shield! They're Gen-" A gunshot echoed through the gateroom and Stackhouse fell to the floor.

The three men opened fire on the control room officers and took them out before they could react and activate the shield.

"Commander," one of the men spoke into his radio, "phase one is complete. We're ready to bring in the rest of the troops."

- - - - -

Elizabeth was still in her office when she heard the gunshots. She put her ear piece back on.

"Col Sheppard, I'm hearing gunfire in the gateroom, I'm not sure what's going on down there."

"Stay where you are; I'm on my way. Elizabeth… stay safe."

Ignoring John's advice, she cautiously left her office and crept along the balcony, staying hidden below the railing. She looked across to the gate controls and gasped when she saw the two officers lying in front of the console. Elizabeth tried to make her way towards the fallen officers, but was quickly surrounded by armed men. They dragged her up by her arms and brought her over to the top of the gateroom staircase, where she came face to face with Commander Kolya.

"Dr. Weir," he smiled coldly.

A chill ran down her spine at the sight of the man, and her whole body tensed with fear. She tried to put on a brave face.

"What the hell do you want?"

Kolya addressed one of his officers. "Bring me Major Sheppard," he scowled, and turned back to Elizabeth. "He will pay for his crimes against the Genii people."

Elizabeth knew this man's ruthlessness and feared for John. She had called him here; if only she could warn him…

"He was defending his team and his city. You would have done the same thing in his position, and you know it!"

"Then you would be free to attempt to take your revenge against me, on behalf of your people, Dr. Weir."

Elizabeth glared. This man was hopeless. "What do you want with us? Surely your government wouldn't have sent all these men for your petty revenge."

"Isn't it obvious? We want this city, so we can better defend ourselves against the Wraith. You're not even of this galaxy - we have more claim to this place than you ever did. Now we choose to stake that claim."

She looked down into the Gateroom and saw bodies of fallen members of her team. _How could they do this? They should have been allies against their common enemy. So many lives lost for this stupidity!_ She felt overcome by a wave of nausea and held onto the railing as her knees buckled. She clung to the hope that her team would find a way out of this. John always found a way.

She watched as more Genii soldiers emerged through the 'gate. Too many, she knew.

Her heart skipped a beat when she saw John being led into the control room by a team of Genii men. His hands were cuffed behind his back and his lip was bloodied and swollen, along with a red welt forming on his cheekbone.

"John!" she called out to him. "Are you ok? What did they do to you?"

"I'm fine," he shrugged it off. "We had a slight disagreement on the subject of handcuffs."

"How nice of you to join us, Major Sheppard," Kolya mocked.

"That's Lieutenant Colonel Sheppard now."

"Oh, well please accept my congratulations," his voice dripped with sarcasm, "short-lived though they may be. We have the city under our control now, with ten times the men we brought last time."

"Oh yeah, remind me of the score last time? Was it something like seventy to one?"

John said it to get under Kolya's skin, but she knew he didn't take any of those deaths lightly.

"Most of your men are already dead, Col. Sheppard, or they will be soon. I think I'll keep her for myself, though."

Elizabeth shuddered as Kolya put his hand around her arm, remembering his arm around her neck pulling her towards the 'gate, that day John had saved her life.

John seethed with rage and a desire to smack that grin off Kolya's smug face, but his hands were cuffed securely behind his back and two Genii soldiers held him in place. He settled for spitting in Kolya's face, a move that earned him a slap that nearly knocked him off his feet.

Elizabeth felt like she'd been struck too. _How dare they? _She couldn't stand to see John in pain and wanted to hold him, protocol be damned.

"Enough. Let's get on with it. Take him," Kolya ordered, and gestured with his gun.

The men obeyed Kolya's orders and roughly shoved John against the wall. He was surrounded by half a dozen Genii men, with guns aimed. How he maintained his veil of defiance and bravery she never knew; he was always strong like that. But at the same time he looked so small and vulnerable, and she wished she could stand by his side.

"What the hell are you doing?" Elizabeth demanded.

"As I said, Col. Sheppard must pay for all the Genii lives he took that day. All those men who never returned to their families."

"I had no choice!" If he had cared to see, Kolya would have seen the pain in John's eyes over those deaths. He hadn't wanted to kill those men, and never took a life casually; only to defend his own people. But blinded by rage, Kolya only saw a murderer of Genii.

"Neither do I." He lashed out and struck John across the face with the butt of his gun. John staggered backwards but didn't fall, as blood trickled down the side of his face.

"Stop this!" Elizabeth cried out, desperately.

"It seems Dr. Weir doesn't want to see you suffer. Would she prefer if we finished this quickly?" Kolya turned to her. "Your choice." He raised his gun to strike John again.

"Stop," she pleaded, knowing what her choice meant.

John groaned as his head was still spinning from the blow. "Kolya… You don't have to do this."

He was unmoved. "You put yourself in this position."

The two men locked eyes and John's glare was intense.

"I could have killed you!"

"Maybe you should have." Kolya aimed his gun.

Elizabeth tried to run to him. What was she going to do, throw herself in front of the bullet? They had plenty more where that came from. It didn't matter, she had to do something, anything. As she struggled against the rough hands that held her back, her eyes met with John's for one brief moment. One look that said so much: _I'm sorry. Take care of each other. I regret…_ - She was almost free! - but it was too late. One shot. Then another, and another. Elizabeth watched as John crumpled to the floor and lay there, motionless. It hit her like a punch in the gut; she felt a wave of dizziness overtake her and gasped for air, willing herself to stand when her body wanted to collapse. At last she broke free of her captors, and this time they let her go because she was no longer a threat.

She ran over to her fallen friend and knelt beside him . "John," she placed a hand on his face. _Get up, John. You always get up. You always come home. _She put her hands on his chest in a hopeless attempt to stop the bleeding, but there was so much…

"Take her to the room over there and tie her up; we'll need her command codes," Kolya ordered.

Elizabeth felt strong hands jerk her up and pull her away from John. "No," she tried to resist. "No!" But she didn't have the strength to fight them. Kolya's men led her into her office and bound her hands to the arms of the chair, then left her there alone.

She'd never felt so alone in her life. When John was with her she'd always felt that somehow they'd pull through, even when all odds were against them. Now she was on her own, with nothing left of him but his blood on her hands.

Her solitude didn't last. She shivered involuntarily as Kolya approached and she strained at her bonds with the urge to violently attack the bastard.

He grinned hatefully. "Now, we're going to have a nice little chat about your command codes."

Elizabeth said nothing.

"You'd better start talking, or you'll end up like your dear Col. Sheppard over there… but it won't be so quick, for you."

"Go to hell." That was all she would say. She wouldn't give him the satisfaction of seeing her rage or her tears. She felt nothing but numbness now; he'd already cut her heart out, what else could he do to hurt her?

Kolya pulled out his knife and brought it close to her face. "You _will_ give me those codes."

She didn't scream as Kolya plunged the knife into her arm.

- - - - -


	3. Chapter 3

**Title:** Waking Dreams  
**Author:** Mer  
**Genre:** General, action/adventure  
**Warnings:** Character death, some violence, a few naughty words  
**Season/Spoilers:** season 1, vaguely season 2, but no spoilers, really  
**Summary:** Kolya and the Genii return to Atlantis in force, seeking revenge and control of the city. Plenty of Shep whumping. (John/Liz friendship, angst)  
**Disclaimer:** I don't own any of the characters. I'm just borrowing them for a bit.

**AN:** Many thanks for all the reviews on my last chapter! And a huge round of applause for Hah and Em for ALL the help they've given me :D I'd also like to blame them for this chapter getting so long I had to split it into two parts, so now there are actually two more chapters coming ;) But the next one is nearly finished so I should have it up soon.

- - - - -

**Waking Dreams**

By Mer 

- Chapter 3 -

_(flashback continued)_

Blood, there was so much… John's blood. Elizabeth watched it saturate the sleeve of her jacket, but her hands were tied and she couldn't stop it; she couldn't save him. The pain brought her back to reality as her numbness lapsed momentarily. No, it was her blood this time…

Kolya was growing frustrated. "We're already in control of the city, Dr. Weir. There is no need for your defiance."

_For John_, she thought. _For all those who died today_. She wasn't going to give in to him.

Kolya struck her across the face and sent the room spinning. "Luckily we have all the time we'll need this time. You'll break eventually."

A voice crackled over his radio and he walked away so Elizabeth couldn't make out much of what was being said.

"Excellent," he spoke into the radio. "No, I want him alive. Bring him to the control room."

He smirked and turned back to Elizabeth. "I think this might help convince you."

She heard him before she saw him. "…I don't have time for this, there are people out there who need my help, _now_ – Elizabeth!"

"Carson!" Her first thoughts were relief that he was alive and unhurt, but she knew this was not going to be good.

"My God, what did they do to you?" Carson tried to move towards her but he was held back. "She needs medical attention, let me go to her!"

"That'll be the least of your concerns soon." Kolya pointed his gun at Carson and turned back to Elizabeth. "How brave are you going to be when it's not just your life at risk, hm? The command codes, or he dies."

No, she couldn't go through this again. John had been military, he'd known the risks… but Carson, he'd had no idea what he was getting into. She saw the fear in his eyes. _Fake codes, give him fake codes_, she though. But that would only delay Kolya for a few minutes and anger him further.

"It's okay, Elizabeth. Don't tell them anything."

"Time's up. Last chance to save your friend, Dr. Weir." She watched him squeeze his finger on the trigger and shut her eyes as she heard a gunshot.

She kept her eyes squeezed shut, not wanting to face the reality, when more gunfire and shouting erupted around her. When she finally opened her eyes, Kolya lay on the floor and a very shocked and frightened Carson was still standing. Major Lorne stood in the doorway, P90 raised. He turned to the two marines with him and ordered them to secure the control room entrance.

"Dr. Weir, let's get you out of here. Are you okay, Ma'am?" he asked as he unbound her wrists.

"Yea, it's nothing…" she replied, still in a state of shock.

"I'll be the judge of that," Carson interrupted, and hurried over to examine her.

Lorne took a field bandage from a pouch on his vest and handed it to Carson. "We've gotta get out of here now. There'll be more Genii here any minute."

Elizabeth stood up slowly as Carson quickly wrapped the bandage around her injured arm. She looked down at Kolya on the floor and it gave her a small relief to see him lying there. She gasped as his eyes shot open and he stared directly at her as he spoke, barely a whisper.

"This…won't make a difference… You've already…lost."

"The control room is secure, let's get moving. Dr. Weir, you know how to use one of these?" Lorne walked over and handed her his Beretta pistol.

Elizabeth took the weapon in her hand. John had taught her how to shoot after her last encounter with Kolya because he thought it would help her feel safe again. She'd agreed because it comforted him - knowing she could protect herself - but she'd never imagined actually taking up a weapon like this. Kolya was still spouting arrogant threats and every time she looked at him she relived John's death. Elizabeth found herself raising her weapon, driven only by her fury that overpowered her natural aversion to violence; she'd deal with the consequences later. She flipped the safety off with her thumb and fired at her target until Lorne put his hand on her shoulder. Kolya didn't speak again.

Lorne stared. "I'll take that as a yes."

Carson's mouth hung open in shock.

"What's our status, Major?" Elizabeth questioned, her face now calm and void of emotion.

"All of the inhabited areas of the city are under Genii control. We've rounded up all the survivors we can find and we're bringing them to the jumper bay. I'm afraid there's nothing more we can do." He paused for a moment. "Dr. Weir, we can't let them take the city."

She knew what he was asking of her. She nodded and let him lead her towards the control console.

_Destroy the city_. Elizabeth knew this was a decision she'd regret for the rest of her life, but what choice did she have? Lorne was right - letting the city fall to the Genii was as bad as letting it fall to the Wraith. They'd give the Wraith the location of Earth in an instant to save their own asses. But to lose this vastness of Ancient knowledge and technology over stupid human pettiness made it hurt even more.

- - - - -

As they walked towards the control panel, Elizabeth fought the urge to turn around and run; run somewhere far from this place and everything that had happened here. She wasn't ready to face what lay near the control console, the friend she had failed - but they needed two command codes to get the job done. There was so much at stake here – Earth, the Milky Way – she had to push her emotions aside and get on with it. She'd done it many times before in negotiations, she could do it once more.

But when she saw him lying there, her carefully built resolve crumbled and she froze, the room spinning around her. _I can't do this_. This wasn't the John she remembered. He looked pale, and broken; surrounded by blood.

"My God," Carson spoke softly, and ran over to John.

Elizabeth followed him and they knelt beside the body of their friend as Carson checked for a pulse. "Can you do anything for him?" she asked with a faint hope, though in her heart she knew the answer.

"I'm sorry." Carson's expression was grim, and she knew this had hit him hard too. He took Elizabeth's hands in his, and she felt a small comfort in this simple gesture which connected her to life when her mind was filled with death. He stood up a moment later and placed a caring hand on her shoulder before going to check for survivors in the control room. Elizabeth stayed beside John's still form and brushed her hand through his hair. _We _will_ take care of each other_.

"Dr. Weir? I've input my codes. We need yours right away so we can get out of here before more Genii show up."

"Yes, of course." She blinked away the tears that were threatening to form in her eyes. She couldn't cry, not now. _Command codes. Concentrate._ Tears would be acknowledging what had happened and she couldn't afford to do that yet or she'd shut down completely. _Focus on your goal._ She typed in her code and held her breath as she hit the button to confirm. _God, what had she done? They were losing so much…_

The countdown flashed onto the screen. Twenty minutes to get out.

Carson returned and reported no other survivors in the control room.

"Alright, let's get moving. We've got twenty minutes to get to the jumper bay and get the hell out of the blast radius."

"Wait," Elizabeth put her hand on his arm. "We can't just leave John here!"

Lorne's expression softened. "I'm sorry ma'am, we just don't have the time and can't afford the extra burden. We've had to leave everyone where they fell…" She looked at him and saw the pain of loss in his eyes too. He lifted up her hand and she felt something cold against her palm; a moment later Major Lorne's stern military façade snapped back into place and he turned away. Elizabeth looked into her hand and grasped onto John's dog tag like it was all she had left in the world.

"We've got Genii on the way!" one of the marines guarding the door reported.

"Let's _move_!" Lorne ordered, and gestured for Elizabeth and Carson to follow the marines.

She took one last look at the gateroom and her fallen friend. _Goodbye, Atlantis. Goodbye, John_.

- - - - -


	4. Chapter 4

**Title:** Waking Dreams  
**Author:** Mer  
**Genre:** General, Action/Adventure, Angst  
**Warnings:** Character death, some violence, a few naughty words  
**Season/Spoilers:** season 1, vaguely season 2, but no spoilers, really  
**Summary:** Kolya and the Genii return to Atlantis in force, seeking revenge and control of the city. Plenty of Shep whumping. (John/Liz friendship, angst)  
**Disclaimer:** I don't own any of the characters. I'm just borrowing them for a bit.

**AN:** Thanks again for your reviews and bearing with me through all the sad bits. This is the last sad chapter and I'll finish off with something a bit more light-hearted :) Thanks again also to Hah and Em for the beta:D

- - - - -

**Waking Dreams**

By Mer 

- Chapter 4 -

_(flashback continued)_

The small group of survivors had nearly made it to the jumper bay when Major Lorne held up his hand, silently signalling them to stop. A single blip flashed on the lifesigns detector, coming from the corridor they were approaching. Lorne raised his P90, peered around the corner cautiously, and came face to face with a gun.

"Ronon!" Elizabeth breathed a sigh of relief.

"I was looking for you," he replied, with an expression she couldn't read.

"You found us. Glad you're okay," she gave him a quick smile. "Ronon, have you seen Teyla?"

"Yeah." …_They were surrounded, they'd have to shoot their way out. They could make it, they had to. But there were too many; she was hit, falling to the ground. There were too many, he couldn't save her…_

His eyes told her everything she needed to know; Teyla wasn't coming with them. She looked to the ground and squeezed her eyes shut. _There would be time to mourn later_, she repeated to herself, as she'd done too many times that day. Elizabeth put her hand on Ronon's arm to let him know it was all right, that it wasn't his fault. She was surprised when he put his other hand on hers and held it tight. They continued on in silence.

"Crap," Lorne whispered harshly. "We've got company. Lots of it." He showed Elizabeth the lifesigns detector; there were at least twenty-five Genii men between them and the jumper bay.

"They can't get into the jumper bay without the gene, so they're waiting to ambush us outside it," Elizabeth realised, and Lorne nodded in agreement.

"Oh, lovely! Now what do we do?" Carson spoke with fear in his voice.

"We're going to have to find another way. There's no way we can get through that many, and we used up all our flashbangs getting to the control room." Lorne frowned and glanced at his watch. _Ten minutes. Not good._

"I can do it." The group turned to look at Ronon as he spoke. "Just stay behind me."

"I don't think so, Ronon. That's suicide. We'll find another way." Elizabeth spoke but she knew he wouldn't hear her. He was already walking towards the bay doors, weapon raised.

He turned back and looked at her. "There _is_ no other way. I'll make them pay for what they did." His walk turned into a run and he vanished around the corner, gun firing. Genii gunfire echoed in the hallway.

"We can't just let him go alone!" Elizabeth pleaded with Lorne, voice panic-stricken.

"I know." Lorne crept towards the corner and signalled the others to follow. Elizabeth gripped her weapon tightly and tried to stop her hands from shaking.

"Dr. Beckett? You've got the gene, I need you to open that jumper bay door the first chance you get."

"Me?" He swallowed hard. "O- okay, I can do that."

When Lorne rounded the corner he was shocked to find Ronon not just still standing, but shooting and tossing Genii soldiers around like ragdolls; blood ran down his arm and leg, but he wasn't slowed down as he fought with rage and a thirst for revenge. Half of the enemy soldiers already lay on the ground.

"Dex, fall back! We've got you covered!" Lorne ordered as he fired at the Genii he could hit without endangering Ronon, but his orders were disregarded. Ronon took out two more men before taking a shot in the chest that made him stagger backwards. He struggled to stand, but kept firing until three more shots knocked him down. This time he didn't move.

"Ronon!" Elizabeth cried out but Lorne held her back, out of the line of fire. She couldn't bear to lose another team member. He was their newest, but he'd just begun to fit in like part of the family. Again she pushed the grief out of her mind and channelled it down to her hands and through her gun as she fired at the soldiers. There were still some Genii men to deal with, but nothing they couldn't handle thanks to Ronon.

As soon as the path was clear, they laid down cover fire while Carson unlocked the jumper bay door and ran through. The others were about to follow when the Genii backup troops arrived.

Five minutes left.

"We've gotta make a run for it. Dr. Weir, keep low and stay behind us while we lay down cover fire." Lorne signalled his men to go and they made a dash for the open door.

The Genii opened fire as soon as the four were out in the open. As they approached the door, Lorne cried out in pain and fell backwards. Elizabeth, standing next to him, tried to break his fall and helped drag him through the doors. They shut and locked the doors as friendly faces guarding the jumper bay greeted them. They'd made it, but at a high price.

"Major Lorne! Are you okay?" Elizabeth crouched beside him and put a hand on his chest.

He tried to sit up and groaned. "Yeah. Just my leg. Help me up." One of the marines guarding the door helped him to his feet and reported that the rest of the survivors were waiting inside the jumper.

Three minutes.

Elizabeth walked into the jumper behind Lorne, as the marine helped him into the pilot's seat. _So few…_ She spotted Rodney among the dozen or so survivors and gave him a small smile. He looked relieved to see her but was too shaken to respond.

"You'll have to let me take a look at that leg, Major." A concerned Carson hovered around Lorne.

"That's going to have to wait 'til after we've cleared the blast. We can't risk going through the gateroom either, the Genii could have dialed in again by now. Please take a seat, doctor." Carson sighed and settled down beside Elizabeth. Lorne turned around to face the group, "Prepare for takeoff."

"Woah, woah, wait!" Rodney stood up. "Where's Sheppard?"

Elizabeth looked up at him and he looked back into her eyes that she had finally allowed to fill with tears. She shook her head softly. Rodney's face fell with a look of shock and devastation as he slowly slumped back into his seat. His mouth moved to speak, but for once he was without words.

Two minutes.

The Jumper took off and the survivors caught their last glimpse of Atlantis, the place that had become their home. Its lights shone against the night sky and rippled across the water, one last cruel reminder of everything they were losing. Carson put his arm around Elizabeth and she leaned on his shoulder and cried until his sleeve was soaked with tears.

One minute.

All they could see was the blackness of space in front of them; the explosion was a blip on the screen, neither felt nor heard. Elizabeth wondered if it had really happened, though Major Lorne assured her sensors indicated the self-destruct had been a success. _So that was it, then._ The remains of Atlantis were falling to the bottom of the ocean, along with the man she'd felt closer to than anyone she'd ever met.

Elizabeth tried to shift her mind to their practical needs as a distraction. They had enough supplies to last a couple of weeks at least, and the Daedalus was due to arrive in nine days. Her mind wandered to how she'd explain the situation to Col. Caldwell while he watched her, judging every bad decision, every way she'd failed her team. There would be families to notify; so many families whose loved ones weren't returning, who would soon feel the way she did. The thoughts tormented her and she struggled to maintain her composure against the overwhelming urge to cry out. The deluge of grief and guilt threatened to drown her and she gasped for air…when she felt something pull her up; a warm touch brushed against her face and made the hairs on the back of her neck stand up. She looked up expectantly, but saw only the walls of the jumper and the silent passengers within. Just her mind playing trick, she sighed. Still, she somehow felt a bit more calm and resolved, and got up to discuss with Lorne their plans for the long wait ahead of them.

- - - - -


	5. Chapter 5

**Title:** Waking Dreams  
**Author:** Mer  
**Genre:** General  
**Warnings:** Character death, some violence, a few naughty words  
**Season/Spoilers:** season 1, vaguely season 2, but no spoilers, really  
**Summary:** Kolya and the Genii return to Atlantis in force, seeking revenge and control of the city. Plenty of Shep whumping. (John/Liz friendship, angst)  
**Disclaimer:** I don't own any of the characters. I'm just borrowing them for a bit.

**AN: **As promised, the sad stuff is over and now it's time for a more lighthearted ending (but not completely so). It got a bit long again, so there's one more chapter to go after this one (she says, for the fifth time...). If you prefer depressing endings, stop reading here :P Thanks again for your great reviews, and to Hah, Em and Beanie for the help! **  
**

- - - - -

**Waking Dreams**

By Mer 

- Chapter 5 -

At first, his world was chaos. He struggled to find his place in it, to create some semblance of order. A concept formed in his mind and he grasped for it: _identity? _His mind grew clearer_; I'm John Sheppard. From Earth. No… from Atlantis?_ Thoughts of those places made him aware of his surroundings, but when he tried to take in the vastness and silence around him he was quickly overwhelmed. _Lost. Alone. Where am I?_

_The transition can be difficult. You must give it time, John. _A voice spoke to him, but he couldn't identify the source. He felt a presence emerging from the silence.

_Transition?_ Memories flooded back to him. _Kolya with a gun pointed at him. Elizabeth's eyes full of panic and tears…he wanted to reach out, to say something to her… Gunshots. Searing pain in his chest… he gasped for air but there was only pain…then darkness._

_I died?_

He tried to let the strange idea sink in. This wasn't what he expected death to be like. To be honest, he had expected nothing; just a darkness that he would never awake from. This was…different. He wasn't quite sure what _this_ was, but there were other concerns pushing to the front of his mind.

_What happened to the others? My friends?_

As if in response to his thoughts, the emptiness fell away and he saw Atlantis; not exactly how he'd seen it in life, but it was there. He could feel the people inside – his friends, the Genii – their fear, their pain… Then there was a flash of light and he could feel it as if he was a part of the city, as it was dying. Everyone he had known, his home, the knowledge of the Ancients, it was all destroyed in an instant. He would have stopped it, but he didn't yet know the power he had to reach out with his mind. All he could do was watch, and grieve. _Elizabeth…_

He felt the presence grow stronger around him until he was at last able to put a name to it. _Chaya?_

_Yes, John. Don't be afraid, you're safe here._

_What about Atlantis? You could have helped them. You could have saved all those people!_

_You know that is not true. You know the rules, we cannot interfere with corporeal matters._

_You didn't seem to mind interfering with me._

_John…_

So, he was ascended now; on a higher plane of existence. His friends were gone, Elizabeth was… It was too much for him to grasp all at once. He sure didn't feel more enlightened.

_Why did you bring me here? If all I can do is watch, you should've let me die with the rest of my friends._

_Not everyone was lost…_

John followed Chaya's thoughts to an object in space. He searched his corporeal memories; a puddlejumper. _There were survivors!_ He let his mind take him towards the jumper; it almost reminded him of flying one. This part, he thought, he could get used to. He took himself inside the ship and felt joy and relief wash over him when he saw Elizabeth there, with Carson and Rodney at her side. John watched her tear-stained face and felt the grief radiate from her and encircle him. It pained him to see her like this and he felt responsible; he wanted to reach out to her, to comfort her any way he could. John imagined himself raising his hand to touch Elizabeth's face and she lifted up her head. _Elizabeth, it's me. I'm okay. You're going to be okay. _For a moment he thought she was looking up at him, but she turned away and her face fell into the same blank expression.

Frustrated, he sought out Chaya again. _Please, send me back. I know you can do that._

John, I can't do that until you have at least experienced more and considered what we have to offer you. You cannot imagine the wonders of this universe… Please, at least give it more thought before you decide.

He admitted to himself it _was_ worth more thought. He longed to return to comfort Elizabeth, but what would she say about his giving up this opportunity so hastily? He'd always admired her spirit of exploration and found it had rubbed off on him more than he'd realised. The knowledge he could acquire could have immeasurable benefits, and those non-interference rules – well, rules could always be bent, couldn't they? The rest of the survivors of his team would take care of Elizabeth; that's what they did. That's what they'd always done. Feeling more resolved, John set a destination in his mind and let himself soar.

------------------------------------------------------------------------------

(Six months later) 

The passage of time in the world of the ascended is not like that of the corporeal world; it's fluid in nature, not precisely measured, and largely ignored. So it was that John Sheppard returned to Earth, unaware of the months that had passed since his death. _Home_, he thought, and wondered if there was still any meaning attached to the word. Strange as it sounded, he'd never felt truly at home until he'd arrived in Atlantis, and there was no going back there…

_Once you have crossed over, you cannot return. Are you certain of your choice?_

_Yes._

_You may choose the place in which to retake your human form._

John let his home world draw him in. From the static noise of billions of souls, he focused on the one that pulled at him with the most force. With one single thought in mind, he let himself fall, towards home, into darkness. _Elizabeth…_

- - - -

Elizabeth was up late reading, again. She still had trouble sleeping, six months later.

Dressed in an immaculate black pantsuit, she stepped behind the podium. She didn't usually dread public speaking, but it was different this time. She didn't want to speak the words that would make it final, she wasn't ready to let go. Elizabeth cleared her throat. "Lt. Col. John Sheppard" - she paused as the words stuck in her throat - "was the heart of the Atlantis mission."

Six months since she'd been in front of the crowd at the memorial service, speaking her public goodbyes to everyone she'd lost; she was still working on the private ones. Though it didn't seem fair to the others, her thoughts usually dwelt on John. Of all the team members she'd grown close to, she'd cared for him the most; more than she'd allowed herself to admit, until he was gone. Of all the deaths she'd witnessed that day, she felt most responsible for his. The events played over and over in her mind – questioning every decision, wondering what she could have done to save him; wondering when she would be able to close her eyes without being tormented by the image of John's lifeless body. The only thoughts powerful enough to repress those images were her most vivid memories of John in life: bright smile and quick wit, never failing to make her smile in return; unwavering strength and selfless courage, comforting her in their darkest hours; hazel green eyes that betrayed the intelligence and emotion he kept carefully hidden below the surface. Though she had been physically attracted to him from the beginning – he was a beautiful man, she admitted – there was so much more to John than met the eye, and she felt she'd only begun to scratch the surface. They'd kept their distance for professional reasons, the right thing to do at the time, but now she was left only with regrets and haunted by what-ifs.

Elizabeth realised that she had been staring at the same page for twenty minutes, and put the book down with a sigh. She got up and wandered to the kitchen to distract herself from her thoughts.

- - - -

John slowly opened his eyes as the universe spun around him, trying to sort out where exactly his place was in it. Shaking off the strange feeling of disorientation, he blinked and tried to move his limbs. _Two arms, ten fingers_…he looked down…_clothing? That's a negative_. At least all his important parts were accounted for. He tried to sit up and smacked his head against something hard and metallic. _Ow. Pain._ He hadn't missed that corporeal feeling.

- - - -

Elizabeth jumped when she heard a noise coming from her bathroom. Not just a noise, but the voice of an intruder in her home. After a moment of panic, she remembered the training she'd had with Teyla during her time on Atlantis and grabbed the nearest object she could brandish as a weapon. Courage gathered, she prepared to face the intruder with a rather large stainless steel pepper grinder in hand. She crept down the hallway and paused outside the bathroom door, taking a deep breath before she flipped on the lights. Instinctively she jumped back and took refuge in the hallway as an equally startled man hid behind her shower curtain. Temporarily blinded by the bright light, she hadn't been able to see much more than the figure of a man in her bathtub. She was pretty sure he wasn't wearing any clothing. _Great_, she thought. _Probably recently escaped from the mental institute._ Elizabeth briefly considered dialing the police, but for some reason felt drawn back into the room instead.

"Who's in there?" she called out cautiously, and added, "I'm armed."

A pair of eyes and a mess of hair peeked around the edge of the curtain.

"What are you going to do, sprinkle pepper on me 'til I sneeze into submission?"

Her guard dropped and her voice softened with tearful awe. "John?"

Elizabeth wondered if her own sanity should be in question as the man that looked like John – her John – reached out for a nearby towel, wrapped it around his waist, and stepped out from behind the curtain. But right now she didn't care if this was a dream, or a hallucination; she ran over and clung to the illusion. He felt real, and whole.

"Elizabeth." This time he hugged her back, and she was shaking as he wrapped his arms around her.

"How…? Is it really you…?" She was overwhelmed with questions, emotions, doubts… She wondered when she would awake from this dream.

"It's me…" A puzzled look crept over his face. "I'm not… quite sure what happened… I think… I died?"

The memories Elizabeth had been carefully pushing away flooded back upon hearing John's words and tried to fight the tears that were forming in her eyes. John saw the pain in her eyes and knew that what he said was true. He tried to reconcile the memories of his life before and his life now.What had happened to him? There was a piece of the puzzle missing, floating on the edge of his consciousness, just out of reach. Right now all that mattered was Elizabeth needed his comfort, and he let her tears fall on his shoulder as he held her close.

In his need to hold Elizabeth, John had forgotten his need to hold up the towel, which chose this moment to drop in a pile around his feet.

His eyes shot open as his face flushed with embarrassment. "…This is kind of awkward."

"Mm-hmm," Elizabeth mumbled in reply, oblivious and wrapped up in the comfort of the embrace.

"Do you..uh.. have anything I could wear?"

"Wear?" She looked up at him. "Oh…" Then she looked down. "_Oh!_" She, too, began to blush and spun around to grab a nearby bathrobe for him. Trying to avert her eyes for the sake of his modesty, she couldn't help but admire his slim, muscular form which she'd never been able to fully appreciate before. John took the robe from her and gave her a little grin while he wrapped himself up in it, as though he knew what she'd been thinking.

Elizabeth led him away from the bathroom and into her living room where they could sit and talk more comfortably. She watched him as he sat and wondered what was going through his mind, beneath his unreadable expression.

"John, what do you remember?"

He looked down at his hands while he contemplated for a minute. "I remember my life before… I remember the Genii, and Kolya…" Elizabeth saw shock and anguish flash in his eyes as the memories of that terrible day returned to him. "I… I wanted to reach out to you, but I was falling… into darkness… then, there was so much confusion, emptiness… and a voice… Chaya."

"Chaya?" She knew John had a connection with the ascended Ancient, and his genes made him closer to an Ancient than anyone else on the expedition…_Was it possible? Had he ascended?_ She could think of no other explanation, and besides, she had heard about Dr. Jackson's ascension.

"John, you ascended?" Her voice was full of awe, and curiosity.

A floodgate in his mind opened and John closed his eyes as memories rushed back to him at a dizzying pace. "Woah." He blinked."That was…weird."

"John, are you okay? What did you remember?"

His eyes were wide with shock and darkened by grief. "Everything."

- - - - -


	6. Chapter 6

**Title:** Waking Dreams  
**Author:** Mer  
**Genre:** General  
**Season/Spoilers:** season 1, vaguely season 2, but no spoilers, really  
**Summary:** Kolya and the Genii return to Atlantis in force, seeking revenge and control of the city. Plenty of Shep whumping. (John/Liz friendship, angst)  
**Disclaimer:** I don't own any of the characters. I'm just borrowing them for a bit.

**AN: **At last, we've reached the end! I had a lot of fun writing it...thanks to all the patient readers, everyone who posted reviews, and of course Hah and Em for beta'ing! Warning - this chapter gets a bit shippy. As much as my cold anti-ship heart can manage ;) Please read and review :D  
COMPLETE

- - - - -

**Waking Dreams**

By Mer 

- Chapter 6 -

John looked pale and shaken, and Elizabeth instinctively put a comforting arm around him. She was silent for a minute, not sure what to say, unable to understand his traumatic experiences.

"Do you want to talk about it?" she eventually managed.

"No…it's okay…"

"John, it's not _okay_ –"

"I mean, I don't think I'm ready yet…not right now."

"I'm sorry, I didn't mean to…"

"No, it's alright, Elizabeth." He licked his lips and tried to change the subject. "…How have you been?"

"Not so good, actually," she confessed.

John's face fell, dragged down by the burden of guilt, and he replied softly, "I'm sorry…" He hesitated, unsure what else to say. He should have been there for her, he told himself. At least he could be here for her now. He gave her a sympathetic look, showing he was here to listen to whatever she needed to say.

"John, you _died_ right in front of me. So many of us never made it home. The fact that I'm talking to you right now is…is…" She shook her head disbelief at the whole situation. "How can I be sure this isn't just a dream?"

"This…" John took her hand in his and held it tight, "…is real." Elizabeth gave him a small smile and looked unconvinced.

"Do you want me to pinch you?" he offered with a grin.

"No…no, that's ok," she rolled her eyes_. Only the real John Sheppard would be such a smartass at a time like this._

Her face darkened as a wave of emotion washed over her; six months of repressed anger, grief and guilt that she finally let flow freely. "Why didn't you let us know you were okay?" she demanded. "We buried you, we grieved for you. I spoke about you at the memorial service! I thought you ascended beings could appear in human form, and if you could come back, why did you wait so long? We were lost without you… I was lost." She immediately regretted her words. He didn't deserve this.

"Elizabeth, I'm so sorry. It's… complicated. I thought, maybe, if I was ascended I could make a difference that way…" Pain of newly recalled memories flickered in his eyes.

"But you couldn't."

"No," he said, voice resonant with sadness. "I couldn't help anyone." John stared out the window, lost in a distant memory. _Wraith hive ships hovered above the tiny sphere of a world, preparing for a culling. Panic radiated from the helpless population below, the terror, wild terror of so many minds. But there was more…He could feel _them_, their terrible hunger. Pleasure, as an appetite was sated, and simultaneously the pain of a life being drained. His mind raged and struck out at them, but the thoughts and images blurred as powerful forces held his powers at bay…_

Elizabeth squeezed his hand and brought him back to the present. "I'm sorry, I shouldn't have said all that. It's just… I missed you, John. More than I can say."

"Me too." He curled his lips into a sweet smile and she felt comforted. He'd always had that effect on her.

"I'm glad you found your way home."

"So am I… Apparently, I'm not cut out for the ascended life." He flashed his trademark crooked grin.

God, she had missed that grin. She couldn't help but crack a smile. "Daniel Jackson lasted a year before they kicked _him_ out," she teased.

"Well, you know me. I can't just sit on my hands and watch…"

"I know." _So why did we do it when it came to our feelings for each other?_ Oh yes, protocol. She couldn't think of any protocols having to do with ascended-descended men who showed up naked in her bathroom…

She looked up and John was looking back at her with those green eyes that she wanted to lose herself in. They were being given a second chance, she realised. _Don't make the same mistake twice_. Impulsively, Elizabeth leaned over and placed a soft kiss on his lips, brushing her hand through his hair as he responded by wrapping his arm around her. _We've waited so long for this_. When she pulled away, John looked stunned and she blushed as she began to regret what she'd done. John sensed her fears and broke the awkward silence.

"Sorry… It's just all a bit weird right now… I'm still getting used to this whole being alive again thing…"

"I'm still getting used to this you being alive again thing…"

"…But it felt good…right." He smiled and she saw in his eyes that he spoke the truth.

"I'll be here when you're ready… and when you're ready to talk about it."

"I know." His smile was warm and he looked more at ease now. "So, you spoke about me at the memorial?"

"Only good things, I promise." She let herself smile back.

They stayed up all night talking about the brighter side of the past six months: Rodney, locked in his lab with the Ancient tech they'd managed to bring home, still hoping for that Nobel prize; Carson, making medical breakthroughs that would make all their sacrifices worth it. They wondered how the rest of the team would react to seeing John again, and he grinned at all the possible ways he could use the opportunity to give Rodney a good scare.

The first light of dawn began to color the sky.

"Hey…you hungry?"

"I haven't eaten in six months."

"Funny," she smirked and got up to go to the kitchen.

She returned with two spoons and a pint of Ben and Jerry's, and watched John's eyes light up. Ice cream had been a rare commodity on Atlantis too.

"So, no ice cream on the higher plane of existence?"

"Nope," John shook his head as he scooped out a large spoonful.

"And they call themselves enlightened."

John laughed and she couldn't help but join him; they'd forgotten how good it felt to laugh. After all this time, they were both glad to be alive again.

- - - - -


End file.
